Some Code
In the annex of reference1.jpg, when i load the page using an include that's where the problems of files been corrupted or missing links.
In the annex of reference2.jpg, instead of using an include to load the php file i placed the download behaviour, still missing to add the upload behavior to this section but so far its working.
I did is copy the same file that has the menus section, header and footer and erased the main content and placed the behaviors requiered for the upload and download.
Take care, and hopefully this might help someone out in the future.
Thanks